QTL analysis with MAGIC population

[Ramesh Bhat]

Dear Dr. Karl,

I have a peanut MAGIC population of 500 lines derived from eight parents with the cross type of risib8.

Is this YAML file okay for risib8?

Also, I am getting the following error, kindly help

Kind regards,

--

Ramesh S. Bhat

Professor and Head
Department of Biotechnology
University of Agricultural Sciences, Dharwad
PIN: 580 005, Dharwad, Karnataka, India
Ph: +91-836-2214457, Mobile: +91-9945667300

email: bha...@uasd.in

[Karl Broman]

"crosstype: magic19" is not right, as you said the cross type was risib8.

Consider the CC example at https://github.com/rqtl/qtl2data/tree/master/CC

karl

[Ramesh Bhat]

Thanks Dr. Karl.

The data are available as zip file (iron.zipand grav2.zip).

Can I find any such zip file and script file for CC example?

Kind regards,

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[Karl Broman]

The files are available at the link I gave you, including as a zip file, cc.zip.

karl

[Ramesh Bhat]

Thanks. I could download that zip file. 

Got the following error

What shall I do?

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[Ramesh Bhat]

Not able to find any cc_pheno.csv in cc.zip. Is this the reason to get the error?

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[Karl Broman]

These data include no phenotypes. I thought they might be useful to you as an example, to structure your own data.

karl

[Ramesh Bhat]

Thanks Dr. Karl.

We have phenotyped the peanut MAGIC population over four seasons. SNP data will be available in about 1-2 months.

Meanwhile, can I get acquainted with the scripts using Arabidopsis 19-way example? 

Later, I would like to analyze our MAGIC population for

1.    QTL and marker for the traits

2.    Effects (additive) for the QTL or the marker

3.    PVE for the QTL/marker

4.    Identifying the parent with the allele having higher mean  

Kind regards,

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[Ramesh Bhat]

Dear Dr. Karl,

I am working with ArabMAGIC.  The following function creates the zip file on my Macbook, but not on my Windows desktop.

zip_datafiles(control_file, "gnutmagic.zip")

Does this require any change?

I got the effects with the following function

c2eff <- scan1coef(pr[,"2"], gnut$pheno[,"height"])

What formula does it consider to calculate the effets here? What do they mean?

Kind regards,

On Sat, Aug 15, 2020 at 1:46 AM Karl Broman <kbr...@gmail.com> wrote:

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[Karl Broman]

I can't tell what is going wrong with zip_datafiles() without further information, such as the exact error message you're getting.

scan1coef() estimates effects via linear regression.

karl

[Ramesh Bhat]

Unfortunately, it does not show any error, but the zip file is not created.

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[Ramesh Bhat]

Dear Dr. Karl,

Can we get the effects and gene annotations for the SNPs using R/qtl2 especially for peanut?

Kind regards,

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